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Data Analysis Tools
QuEST – ChIP-seq data analysis package
HOMER – Hypergeometric Optimization of Motif Enrichment — ChIP-seq and Motif Discovery
Bowtie – An ultrafast memory-efficient short read aligner
Tophat – A spliced read mapper for RNA-Seq
Cufflinks – Transcript assembly, differential expression, and differential regulation for RNA-Seq
Primer-BLAST – primer designing tool for qPCR and qRT-PCR
DAVID – Database for Annotation, Visulatization and Integrated Discovery – Gene annotation
SEQanswers — Forum for next gen sequencing users